[English] 日本語
Yorodumi- PDB-8olw: Structure of Oceanobacillus iheyensis group II intron before the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8olw | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Oceanobacillus iheyensis group II intron before the first step of splicing in the presence of K+, Ca2+ and intronistat B | |||||||||||||||||||||||||||
Components | Group IIC intron | |||||||||||||||||||||||||||
Keywords | RNA / RIBOZYME / METALLOENZYME / SELF-SPLICING / RETROTRANSPOSITION | |||||||||||||||||||||||||||
Function / homology | : / RNA / RNA (> 10) / RNA (> 100) Function and homology information | |||||||||||||||||||||||||||
Biological species | Oceanobacillus iheyensis (bacteria) | |||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å | |||||||||||||||||||||||||||
Authors | Silvestri, I. / Marcia, M. | |||||||||||||||||||||||||||
Funding support | France, Italy, 8items
| |||||||||||||||||||||||||||
Citation | Journal: Nat Commun / Year: 2024 Title: Targeting the conserved active site of splicing machines with specific and selective small molecule modulators Authors: Silvestri, I. / Manigrasso, J. / Andreani, A. / Brindani, N. / Mas, C. / Reiser, J.B. / Vidossich, P. / Martino, G. / McCarthy, A. / De Vivo, M. / Marcia, M. | |||||||||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8olw.cif.gz | 454.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8olw.ent.gz | 367.4 KB | Display | PDB format |
PDBx/mmJSON format | 8olw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8olw_validation.pdf.gz | 410.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8olw_full_validation.pdf.gz | 464.9 KB | Display | |
Data in XML | 8olw_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 8olw_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/8olw ftp://data.pdbj.org/pub/pdb/validation_reports/ol/8olw | HTTPS FTP |
-Related structure data
Related structure data | 8olsC 8olvC 8olyC 8olzC 8om0C 8ruhC 8ruiC 8rujC 8rukC 8rulC 8rumC 8runC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: RNA chain | Mass: 128549.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oceanobacillus iheyensis (bacteria) | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-K / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.8 % |
---|---|
Crystal grow | Temperature: 303.15 K / Method: vapor diffusion, hanging drop Details: 100 mM potassium acetate, 100 mM potassium chloride, 100 mM calcium chloride, 50 mM HEPES sodium, pH 7.0, 4.5% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 4→48.68 Å / Num. obs: 16065 / % possible obs: 97.77 % / Redundancy: 4.6 % / CC1/2: 1 / Rmerge(I) obs: 0.097 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 4→4.1 Å / Num. unique obs: 1442 / CC1/2: 0.28 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→48.68 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.969 / SU B: 184.611 / SU ML: 1.038 / Cross valid method: THROUGHOUT / ESU R Free: 0.785 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 212.388 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 4→48.68 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|